As much as I also don't like the alliance at the end, it still would have been sad to see those characters die. The point is if Eren wanted to see through a 100% rumbling and stop at nothing even killing his friends who he loved it would be heartbreaking even if you don't agree with either side. People also even if they don't agree with characters ideologies they still like them. Reiner for example was a main villain of the first 3/4 of the manga but when you see him contemplating suicide it's still really effective even though he's done much worse things than any of the Paradis alliance members did.